Class Prediction with Microarray Datasets

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Documentation for package `CPEg' version 1.1

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AllDA Run battery of classification algorithms
Alon Colon cancer data set of Alon et al. 1999
BootCP Bootstrap estimate of mis-classification rates
BRAC1 Breast cancer, BRCA1 mutation, Hendenfalk et al. 2004
BRAC2 Breast cancer, BRCA2 mutation, Hendenfalk et al. 2004
cv.rda Utility function, FitRDA
ErrorPredClass Utility function, FitNNReg
FitCART Classification using CART
FitDLDA Diagonal Linear DA
FitDQDA Diagonal Quadratic DA
FitFFNN Feed Forward Neural Net for Classification
FitkNN NN classification
FitLDA LDA
FitLogistic Logistic regression classification
FitNNReg Classification using NN covariates
FitPCReg Principal component regression
FitQDA QDA
FitRDA Regularized Discriminant Analysis
FitRPLS RPLS
FitSVM Support Vector Machine Classification
Gaussian Gaussian data with two classes
GeneSelect Select supergenes
GeneSelectPValue Select supergenes using p-value
Golub Acute leukemia data set, Golub et al. 1999
Iizuka Iizuka carcinoma data set
ImagePlot Image plot of design matrix
KNN.covariate.test KNN autocovariates, test data
KNN.covariate.train KNN autocovariates, training data
kNNSelect Use leave-one-out CV to select k
Mixture HTF Mixture Classifcation Example
mrate mis-classification rate
NN.CV Cross validation error rate
NN.K Test class, utility function
Nutt High-grade glioma dataset, Nutt et al., 2003
OneDPlots One dimension data plots of the columns
OptimalK Optimal K
OrderVar.glm NN using BIC
Singh Prostate cancer data set, Singh et al. 2002
Spira Smoker dataset, Spira et al. 2004
Sporadic Breast cancer, Sporadic mutation, Hendenfalk et al. 2004
Standardize Standarize matrix
TTestTable Table of p-values using t-test
Veer Breast cancer data set, Van't Veer et al., 2002